Fig. 5

Somatic copy number gain and loss profiling from PDX SNP array data. a Overview of the copy number alteration and loss of heterozygosity prediction workflow for SNP array data from PDX tumors (see Methods for details). b Comparison of copy number for ovarian cancer PDX TM00327 relative to the estimated overall cancer genome ploidy of the PDX sample or the diploid state between analyses with and without paired-normal. The log₂(CN/ploidy) gives the best agreement for comparing copy number analyzed with and without paired-normal. (CN-2: copy number difference relative to diploid state; CN/2: copy number ratio relative to diploid state, CN-ploidy: copy number difference relative to overall cancer genome ploidy, CN/ploidy: copy number ratio relative to overall cancer genome ploidy). c Mean expression fold change of genes with normal copy number, copy number gain (log₂(CN/ploidy) > 1) and copy number loss (log₂(CN/ploidy) < − 1) state for a selected list of known oncogenes that are amplified in cancers and for known tumor suppressor genes that are deleted in cancers from the Cancer Gene Census [57]. Over-expressed and under-expressed genes marked with * indicates significant differences in expression fold change with copy number gain or loss state respectively relative to the normal state across all PDX samples